Single Cell Analysis Python Packages

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

48K 266 27

scimap

Spatial Single-Cell Analysis Toolkit

13K 111 36

pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

8K 384 36

spacr

spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)

5K 6 1

celescope

Single Cell Analysis Pipelines

4K 119 36

qpsphere

Python library for spheres in quantitative phase imaging

4K 6 2

cytotable

Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

3K 19 6

spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

1K 23 2

spacr-nightly

Spatial phenotype analysis of crisp screens (SpaCr)

1K 6 0

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

1K 6 2

pypairs

PyPairs - A python scRNA-Seq classifier

1K 3 4

sctape

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

934 61 11

mnnpy

Mutual nearest neighbors correction in python.

684 77 34

scportrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

655 108 8

transmorph

A unifying data integration framework.

642 11 2

cosg

Accurate and fast cell marker gene identification with COSG

443 59 7

vipcca

Single-cell alignment

413 9 3

smprofiler

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

311 23 2

pyspade

Single cell Perturbations - Analysis of Differential gene Expression

293 8 0

ccsf

Leveraging cell-cell similarity for high-performance spatial and temporal cellular mappings from gene expression data (Cell Patterns, 2023)

274 1 2

featuremap

FeatureMAP (Feature-preserving Manifold Approximation and Projection) is an interpratable dimensionality reduction tool.

271 13 1

scouts

Single Cell Outlier Selector - quickly find outliers in your single-cell data

251 3 0

scslat

A graph deep learning based tool to align single cell spatial omics data

250 92 8

emergene

EMERGENE for individual cell-based differential transcriptomic analysis across conditions.

231 3 0